dot-get_mean_ratio2: Get Mean Ratio for Each Gene x Cell Type (Old internal...

In LieberInstitute/DeconvoBuddies: Helper Functions for LIBD Deconvolution

Get Mean Ratio for Each Gene x Cell Type (Old internal version)

Description

Calculate the mean ratio value and rank for each gene for each cell type in the sce object, to identify effective marker genes for deconvolution.

Usage

.get_mean_ratio2(
  sce,
  cellType_col = "cellType",
  assay_name = "logcounts",
  add_symbol = TRUE
)

Arguments

sce	SummarizedExperiment-class object
cellType_col	A character(1) name of the column in the colData() of sce that denotes the cell type or group of interest
assay_name	A character(1) specifying the name of the assay() in the sce object to use to rank expression values. Defaults to logcounts since it typically contains the normalized expression values.
add_symbol	a logical indicating whether the gene symbol column to the marker stats table

Details

Improved efficiency and ability to handle large data sets from get_mean_ratio().

Value

Table of mean ratio for each x cell type

Examples

#' ## load example SingleCellExperiment
if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")

## Get the mean ratio for each gene for each cell type defined in `cellType_broad_hc`
.get_mean_ratio2(sce_DLPFC_example, cellType_col = "cellType_broad_hc")

#  gene       cellType.target mean.target cellType    mean ratio rank_ratio anno_ratio
#<chr>      <fct>                 <dbl> <fct>      <dbl> <dbl>      <int> <chr>
# 1 CD22       Oligo                  1.36 OPC       0.0730  18.6          1 Oligo/OPC: 18.625
# 2 LINC01608  Oligo                  2.39 Micro     0.142   16.8          2 Oligo/Micro: 16.829
# 3 FOLH1      Oligo                  1.59 OPC       0.101   15.7          3 Oligo/OPC: 15.684
# 4 SLC5A11    Oligo                  2.14 Micro     0.145   14.7          4 Oligo/Micro: 14.697
# 5 AC012494.1 Oligo                  2.42 OPC       0.169   14.3          5 Oligo/OPC: 14.282

LieberInstitute/DeconvoBuddies documentation built on Dec. 16, 2024, 10:32 p.m.